Receptivity to Library Involvement in Scientific Data Curation: A Case Study at the University of Colorado Boulder

Increasingly libraries are expected to play a role in scientific data curation initiatives, i.e., the management and preservation of digital data over the long-term. This case study offers a novel approach for identifying researchers who are receptive toward library involvement in data curation. The authors interviewed researchers at the University of Colorado Boulder and, after analysis, created eight design personas. Each persona represents an aggregation of researcher attributes and can be used to target strategic relationships for nascent or emerging data management initiatives. These personas are applicable to any academic library seeking to provide data curation support

Integrating the social studies and language arts curriculum through a literature-based program focused on the Civil War

Integrating the concepts and processes of the curricular areas in the elementary school can enhance students\u27 learning. This integration can extend children\u27s thinking-language abilities and their understanding of content. Children\u27s literature can facilitate the integration of the language arts and social studies areas. Historical fiction pieces, full length and picture books, can especially enrich the study of the Civil War. This article includes a review of literature on the integration of the school program through literature and a literature base with accompanying activities that integrates the language arts into a social studies unit on the American Civil War

Life at low Reynolds number Re-visited: The efficiency of microbial propulsion

It has for over 40 years been taken as a truth universally acknowledged that microbial swimming efficiency by flagellar propulsion is fixed by fluid mechanical limitations at 1–2%. And that the missing 98% dissipated as heat is inefficient or wasted. Estimates of such low swimming efficiency make no sense. Microbes have had billions of years to evolve highly efficient swimming; images of microbes in motion show movement with alacrity and maximum speeds of up to 10 body lengths per second, equivalent to the running and swimming speeds of far larger animals. This paradox can be resolved by taking into account the hydrogen-bonded nature of water and how efficient viscous flow over the surface of the animal is established. The minimal requirement for viscous flow is that the activation energy barrier be overcome. The activation energy for viscous flow in water and sea water is the amount of energy required to break 2 hydrogen bonds—breaking apart the dominant water pentamer into the single H2O species, thus greatly reducing the size of the molecular hole required for flow. Microbial swimming efficiency is made highly efficient by devoting some 95% of the energy expended (some must be lost to entropy) into the breaking of hydrogen bonds

Life at low Reynolds Number Re-visited: The apparent activation energy of viscous flow in sea water

In a 1976 lecture entitled “Life at low Reynolds Number,” Edward Purcell examined constraints on mobility of small aquatic animals defining the energetic challenge as “to move far enough to beat diffusion.” We show that the essential requirement is the need to do sufficient work to overcome the activation energy of viscous flow. Raman spectroscopy shows that sea water is dominated (78–85%) by the hydrogen bonded forms, primarily as the large (H2O)5 tetrahedral pentamer form. Two hydrogen bonds must be broken to disrupt this structure. The strength of the hydrogen bond in water is ~8.4 kJ/mol and the experimentally determined activation energy of viscous flow (~16.7 kJ/mol) is approximately equal to that required to break two hydrogen bonds in water. For viscous flow to occur a molecular vacancy must form for a flowing molecule to move into; the smaller the vacancy needed the less energy required. The heat created by a small animal swimming breaks hydrogen bonds thus forming a layer of small non-hydrogen bonded H2O molecules around the animal. These “lubricate” the surface yielding far more efficient viscous flow. The activation energy of the viscous flow of water decreases with pressure most likely due to the weaker strength of the hydrogen bond under pressure – lab and field data support this observation. The dissipation of tidal energy as heat, often attributed to “intermolecular forces,” is directly related to the breaking of hydrogen bonds

Access to Online Historical Aerial Photography Collections: Past Practice, Present State, and Future Opportunities

The authors review how access to historical aerial photograph collections has evolved in response to technological developments and addresses areas for further advancement, with a particular emphasis on developing, preserving, and sustaining online collections. The authors focus specifically on the areas of metadata, the Semantic Web and linked data, and sustainability through collaboration. The article includes brief case studies, highlighting various projects involving the aerial photography collections at the University of Minnesota. The conclusion asserts the critical role played by geographic information librarians in effectively carrying out the strategies described in the article as they relate to the long-term sustainability of digital geospatial collections

Extraction of the resonance parameters at finite times

In this paper we propose a model-independent method to extract the resonance parameters on the lattice directly from the Euclidean 2-point correlation functions of the field operators at finite times. The method is tested in case of the two-point function of the Delta-resonance, calculated at one loop in Small Scale Expansion. Further, the method is applied to a 1+1-dimensional model with two coupled Ising spins and the results are compared with earlier ones obtained by using Luescher's approach.Comment: 20 pages, 6 figure

Patterns and rates of exonic de novo mutations in autism spectrum disorders

Autism spectrum disorders (ASD) are believed to have genetic and environmental origins, yet in only a modest fraction of individuals can specific causes be identified1,2. To identify further genetic risk factors, we assess the role of de novo mutations in ASD by sequencing the exomes of ASD cases and their parents (n= 175 trios). Fewer than half of the cases (46.3%) carry a missense or nonsense de novo variant and the overall rate of mutation is only modestly higher than the expected rate. In contrast, there is significantly enriched connectivity among the proteins encoded by genes harboring de novo missense or nonsense mutations, and excess connectivity to prior ASD genes of major effect, suggesting a subset of observed events are relevant to ASD risk. The small increase in rate of de novo events, when taken together with the connections among the proteins themselves and to ASD, are consistent with an important but limited role for de novo point mutations, similar to that documented for de novo copy number variants. Genetic models incorporating these data suggest that the majority of observed de novo events are unconnected to ASD, those that do confer risk are distributed across many genes and are incompletely penetrant (i.e., not necessarily causal). Our results support polygenic models in which spontaneous coding mutations in any of a large number of genes increases risk by 5 to 20-fold. Despite the challenge posed by such models, results from de novo events and a large parallel case-control study provide strong evidence in favor of CHD8 and KATNAL2 as genuine autism risk factors

An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge

There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. RESULTS: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. CONCLUSIONS: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups

New insights into the genetic etiology of Alzheimer's disease and related dementias

Characterization of the genetic landscape of Alzheimer's disease (AD) and related dementias (ADD) provides a unique opportunity for a better understanding of the associated pathophysiological processes. We performed a two-stage genome-wide association study totaling 111,326 clinically diagnosed/'proxy' AD cases and 677,663 controls. We found 75 risk loci, of which 42 were new at the time of analysis. Pathway enrichment analyses confirmed the involvement of amyloid/tau pathways and highlighted microglia implication. Gene prioritization in the new loci identified 31 genes that were suggestive of new genetically associated processes, including the tumor necrosis factor alpha pathway through the linear ubiquitin chain assembly complex. We also built a new genetic risk score associated with the risk of future AD/dementia or progression from mild cognitive impairment to AD/dementia. The improvement in prediction led to a 1.6- to 1.9-fold increase in AD risk from the lowest to the highest decile, in addition to effects of age and the APOE ε4 allele